Human Gene HMGN5 (ENST00000358130.7_8) from GENCODE V47lift37
  Description: high mobility group nucleosome binding domain 5 (from RefSeq NM_030763.3)
Gencode Transcript: ENST00000358130.7_8
Gencode Gene: ENSG00000198157.11_13
Transcript (Including UTRs)
   Position: hg19 chrX:80,369,198-80,457,412 Size: 88,215 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chrX:80,370,148-80,377,048 Size: 6,901 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:80,369,198-80,457,412)mRNA (may differ from genome)Protein (282 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HMGN5_HUMAN
DESCRIPTION: RecName: Full=High mobility group nucleosome-binding domain-containing protein 5; AltName: Full=Nucleosome-binding protein 1;
FUNCTION: Preferentially binds to euchromatin and modulates cellular transcription by counteracting linker histone-mediated chromatin compaction (By similarity).
SUBCELLULAR LOCATION: Nucleus. Note=Associates with nucleosomes in euchromatin and is largely excluded from constitutive heterochromatin (By similarity).
TISSUE SPECIFICITY: Ubiquitously expressed.
DOMAIN: Specifically targeted by its C-terminus to nucleosomes in euchromatin (By similarity).
SIMILARITY: Belongs to the HMGN family.
SEQUENCE CAUTION: Sequence=AK094058; Type=Frameshift; Positions=132;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 35.97 RPKM in Testis
Total median expression: 234.15 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -72.60300-0.242 Picture PostScript Text
3' UTR -163.70950-0.172 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000079 - HMGN_fam

Pfam Domains:
PF01101 - HMG14 and HMG17

ModBase Predicted Comparative 3D Structure on P82970
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003723 RNA binding
GO:0031492 nucleosomal DNA binding

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0008284 positive regulation of cell proliferation
GO:0010628 positive regulation of gene expression
GO:0043066 negative regulation of apoptotic process
GO:0045893 positive regulation of transcription, DNA-templated
GO:0071157 negative regulation of cell cycle arrest

Cellular Component:
GO:0000785 chromatin
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AF250329 - Homo sapiens nucleosomal binding protein 1 (NSBP1) mRNA, complete cds.
JD394263 - Sequence 375287 from Patent EP1572962.
JD095776 - Sequence 76800 from Patent EP1572962.
JD300169 - Sequence 281193 from Patent EP1572962.
JD038327 - Sequence 19351 from Patent EP1572962.
JD285096 - Sequence 266120 from Patent EP1572962.
BC005342 - Homo sapiens nucleosomal binding protein 1, mRNA (cDNA clone MGC:12433 IMAGE:3838879), complete cds.
AK094058 - Homo sapiens cDNA FLJ36739 fis, clone UTERU2013262.
AX748432 - Sequence 1957 from Patent EP1308459.
JD331396 - Sequence 312420 from Patent EP1572962.
EU446988 - Synthetic construct Homo sapiens clone IMAGE:100070082; IMAGE:100012197; FLH257429.01L nucleosomal binding protein 1 (NSBP1) gene, encodes complete protein.
AK315792 - Homo sapiens cDNA, FLJ96911, highly similar to Homo sapiens nucleosomal binding protein 1 (NSBP1), mRNA.
KJ894678 - Synthetic construct Homo sapiens clone ccsbBroadEn_04072 HMGN5 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000358130.1, ENST00000358130.2, ENST00000358130.3, ENST00000358130.4, ENST00000358130.5, ENST00000358130.6, HMGN5_HUMAN, NM_030763, NSBP1, P82970, Q5JSL1, uc318ajy.1, uc318ajy.2
UCSC ID: ENST00000358130.7_8
RefSeq Accession: NM_030763.3
Protein: P82970 (aka HMGN5_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.